鱼类特异的基因组复制

辐鳍鱼类是脊椎动物中种类最多、分布最广的类群,其基因组大小不等。过去的观点认为,在脊椎动物进化历程中曾发生了两次基因组复制。近期的系统基因组学研究资料进一步提出,在大约350百万年,辐鳍鱼还发生了第三次基因组复制,即鱼类特异的基因组复制(fish-specificgenomeduplication,FSGD),且发生的时间正处在“物种极度丰富”的硬骨鱼谱系(真骨总目)和“物种贫乏”的谱系(辐鳍鱼纲基部的类群)出现分歧的时间点,表明FSGD与硬骨鱼物种和生物多样性的增加有关。进一步开展鱼类比较基因组学和功能基因组学研究将进一步验证FSGD这一假说。     

Prey Capture in Actinopterygian Fishes: A Review of Suction Feeding Motor Patterns with New Evidence from an Elopomorph Fish, Megalops atlanticus

Suction feeding is recognized as the dominant mode of aquaticprey capture in fishes. While much work has been done identifyingmotor pattern variations of this behavior among diverse groupsof actinopterygian fishes, many ray-finned groups are stillnot represented. Further, the substantial amount of inherentvariation in electromyography makes much of the pioneering workof suction feeding motor patterns in several basal groups insufficientfor evolutionary comparisons. Robust evolutionary comparisonshave identified conserved qualitative traits in the order ofmuscle activation during suction feeding (jaw opening > buccalcavity expansion > jaw closing). However, quantitative traitsof suction motor patterns (i.e., burst durations and relativeonset times) have changed over evolutionary time among actinopterygianfishes. Finally, new motor pattern evidence is presented froma previously neglected group, the Elopomorpha. The results suggestthat future investigations of the muscles influencing lateralexpansion of the mouth cavity and head anatomy may provide valuablenew insights into the evolution of suction feeding motor patternsin ray-finned fishes. In addition, the evidence illustratesthe value of comprehensive EMG surveys of cranial muscle activitiesduring suction feeding behavior.     

Evolution of levers and linkages in the feeding mechanisms of fishes

The evolution of feeding mechanisms in the ray-finned fishes(Actinopterygii) is a compelling example of transformation ina musculoskeletal complex involving multiple skeletal elementsand numerous muscles that power skull motion. Biomechanicalmodels of jaw force and skull kinetics aid our understandingof these complex systems and enable broad comparison of feedingmechanics across taxa. Mechanical models characterize how musclesmove skeletal elements by pulling bones around points of rotationin lever mechanisms, or by transmitting force through skeletalelements connected in a linkage. Previous work has focused onthe feeding biomechanics of several lineages of fishes, buta broader survey of skull function in the context of quantitativemodels has not been attempted. This study begins such a surveyby examining the diversity of mechanical design of the oraljaws in 35 species of ray-finned fishes with three main objectives:(1) analyze lower jaw lever models in a broad phylogenetic rangeof taxa, (2) identify the origin and evolutionary patterns ofchange in the linkage systems that power maxillary rotationand upper jaw protrusion, and (3) analyze patterns of changein feeding design in the context of actinopterygian phylogeny.The mandibular lever is present in virtually all actinopterygians,and the diversity in lower jaw closing force transmission capacity,with mechanical advantage ranging from 0.04 to 0.68, has importantfunctional consequences. A four-bar linkage for maxillary rotationarose in the Amiiformes and persists in various forms in manyteleost species. Novel mechanisms for upper jaw protrusion basedon this linkage for maxillary rotation have evolved independentlyat least five times in teleosts. The widespread anterior jawslinkage for jaw protrusion in percomorph fishes arose initiallyin Zeiformes and subsequently radiated into a wide range ofpremaxillary protrusion capabilities.     

Symposium Summary: Evolutionary Patterns in Actinopterygian Fishes

SYNOPSIS. The actinopterygian fishes are an exemplary cladefor the study of structural and functional evolutionary patterns.With over half of all vertebrate species, ray-finned fisheshave diversified into a wide variety of habitats, and considerableprogress has been made over the last fifteen years in understandingthe genealogical relationships of actinopterygians. This symposiumhas contributed to our understanding of phylogenetic patternsin actinopterygians and to knowledge of the major structuraland functional patterns in locomotor, auditory, trophic, andneural systems. A number of key areas for future research havebeen identified. (1) The relationships of "palaeonisciform"fishes, (2) the study of trends in feeding and locomotor systemswithin a phylogenetic context, (3) the identification of primitivepatterns of pharyngeal jaw movement and steady and unsteadylocomotor patterns in actinopterygians, (4) the homologies,identification, and functional significance of neural pathwaysin the telencephalon, and (5) the comparative study of form-functionrelations in the auditory system. The study of teleost fishbiology has proceeded at the expense of data on primitive actinopterygians(e.g., Polypterus, Polyodon, Aapenser, Lepisosteus, Amia) whichare especially important in the analysis of structural and functionalpatterns in ray-finned fishes.     

From 2R to 3R: evidence for a fish-specific genome duplication (FSGD)

An important mechanism for the evolution of phenotypic complexity, diversity and innovation, and the origin of novel gene functions is the duplication of genes and entire genomes. Recent phylogenomic studies suggest that, during the evolution of vertebrates, the entire genome was duplicated in two rounds (2R) of duplication. Later, approximately 350 mya, in the stem lineage of ray-finned (actinopterygian) fishes, but not in that of the land vertebrates, a third genome duplication occurred-the fish-specific genome duplication (FSGD or 3R), leading, at least initially, to up to eight copies of the ancestral deuterostome genome. Therefore, the sarcopterygian (lobe-finned fishes and tetrapods) genome possessed originally only half as many genes compared to the derived fishes, just like the most-basal and species-poor lineages of extant fishes that diverged from the fish stem lineage before the 3R duplication. Most duplicated genes were secondarily lost, yet some evolved new functions. The genomic complexity of the teleosts might be the reason for their evolutionary success and astounding biological diversity.     

Expression of the FGF-related proto-oncogene int-2 during gastrulation and neurulation in the mouse.

The proto-oncogene int-2 has been implicated in the formation of mouse mammary-tumour-virus-induced mammary tumours. Analysis of the predicted coding sequence indicates that int-2 is a member of the fibroblast growth factor family. Previous studies using Northern blot analysis suggested that normal expression of int-2 may be confined to extra-embryonic endoderm lineages of embryonic stages of mouse development. We have used in situ hybridization and Northern blot analysis to examine directly int-2 expression in embryo stem cells and in the developing embryo from early gastrulation to midsomite stages. Complex patterns of accumulation of int-2 RNA were observed in embryonic and extra-embryonic tissues. The data suggest multiple roles for int-2 in development which may include migration of early mesoderm cells and induction of the otocyst.     

Evolution of the dorsal-ventral patterning network in the mosquito, Anopheles gambiae

The dorsal-ventral patterning of the Drosophila embryo is controlled by a well-defined gene regulation network. We wish to understand how changes in this network produce evolutionary diversity in insect gastrulation. The present study focuses on the dorsal ectoderm in two highly divergent dipterans, the fruitfly Drosophila melanogaster and the mosquito Anopheles gambiae. In D. melanogaster, the dorsal midline of the dorsal ectoderm forms a single extra-embryonic membrane, the amnioserosa. In A. gambiae, an expanded domain forms two distinct extra-embryonic tissues, the amnion and serosa. The analysis of approximately 20 different dorsal-ventral patterning genes suggests that the initial specification of the mesoderm and ventral neurogenic ectoderm is highly conserved in flies and mosquitoes. By contrast, there are numerous differences in the expression profiles of genes active in the dorsal ectoderm. Most notably, the subdivision of the extra-embryonic domain into separate amnion and serosa lineages in A. gambiae correlates with novel patterns of gene expression for several segmentation repressors. Moreover, the expanded amnion and serosa anlage correlates with a broader domain of Dpp signaling as compared with the D. melanogaster embryo. Evidence is presented that this expanded signaling is due to altered expression of the sog gene.     

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.     

Genome Duplications and Accelerated Evolution of Hox Genes and Cluster Architecture in Teleost Fishes

The early origin of four vertebrate Hox gene clusters duringthe evolution of gnathostomes was likely caused by two consecutiveduplications of the entire genome and the subsequent loss ofindividual genes. The presumed conserved and important rolesof these genes in tetrapods during development led to the generalassumption that Hox cluster architecture had remained unchangedsince the last common ancestor of all jawed vertebrates. Butrecent data from teleost fishes reveals that this is not thecase. Here, we present an analysis of the evolution of vertebrateHox genes and clusters, with emphasis on the differences betweenthe Hox A clusters of fish (actinopterygian) and tetrapod (sarcopterygian)lineages. In contrast to the general conservation of genomicarchitecture and gene sequence observed in sarcopterygians,the evolutionary history of actinopterygian Hox clusters likelyincludes an additional (third) genome duplication that initiallyincreased the number of clusters from four to eight. We document,for the first time, higher rates of gene loss and gene sequenceevolution in the Hox genes of fishes compared to those of landvertebrates. These two observations might suggest that two differentmolecular evolutionary strategies exist in the two major vertebratelineages. Preliminary data from the African cichlid fish Oreochromisniloticus compared to those of the pufferfish and zebrafishreveal important differences in Hox cluster architecture amongfishes and, together with genetic mapping data from Medaka,indicate that the third genome duplication was not zebrafish-specific,but probably occurred early in the history of fishes. Each descendingfish lineage that has been characterized so far, distinctivelymodified its Hox cluster architecture through independent secondarylosses. This variation is related to the large body plan differencesobserved among fishes, such as the loss of entire sets of appendagesand ribs in some lineages.     

Uncoupled embryonic and extra-embryonic tissues compromise blastocyst development after somatic cell nuclear transfer

Somatic cell nuclear transfer (SCNT) is the most efficient cell reprogramming technique available, especially when working with bovine species. Although SCNT blastocysts performed equally well or better than controls in the weeks following embryo transfer at Day 7, elongation and gastrulation defects were observed prior to implantation. To understand the developmental implications of embryonic/extra-embryonic interactions, the morphological and molecular features of elongating and gastrulating tissues were analysed. At Day 18, 30 SCNT conceptuses were compared to 20 controls (AI and IVP: 10 conceptuses each); one-half of the SCNT conceptuses appeared normal while the other half showed signs of atypical elongation and gastrulation. SCNT was also associated with a high incidence of discordance in embryonic and extra-embryonic patterns, as evidenced by morphological and molecular "uncoupling". Elongation appeared to be secondarily affected; only 3 of 30 conceptuses had abnormally elongated shapes and there were very few differences in gene expression when they were compared to the controls. However, some of these differences could be linked to defects in microvilli formation or extracellular matrix composition and could thus impact extra-embryonic functions. In contrast to elongation, gastrulation stages included embryonic defects that likely affected the hypoblast, the epiblast, or the early stages of their differentiation. When taking into account SCNT conceptus somatic origin, i.e. the reprogramming efficiency of each bovine ear fibroblast (Low: 0029, Med: 7711, High: 5538), we found that embryonic abnormalities or severe embryonic/extra-embryonic uncoupling were more tightly correlated to embryo loss at implantation than were elongation defects. Alternatively, extra-embryonic differences between SCNT and control conceptuses at Day 18 were related to molecular plasticity (high efficiency/high plasticity) and subsequent pregnancy loss. Finally, because it alters re-differentiation processes in vivo, SCNT reprogramming highlights temporally and spatially restricted interactions among cells and tissues in a unique way.     

Cadherin-mediated cell interaction regulates germ cell determination in mice

The germ cell lineage segregates from the somatic cell lineages in early embryos. Germ cell determination in mice is not regulated by maternally inherited germplasm, but is initiated within the embryo during gastrulation. However, the mechanisms of germ cell specification in mice remain unknown. We located precursors to primordial germ cells (PGCs) within early embryos, and show here that cell-cell interaction among these precursors is required for germ cell specification. We found that the expression of a calcium-dependent cell adhesion molecule, E-cadherin, is restricted to the proximal region of extra-embryonic mesoderm that contains PGC precursors, and that blocking the functions of E-cadherin with an antibody inhibits PGC formation in vitro. These results showed that E-cadherin-mediated cell-cell interaction among cells containing PGC precursors is essential to directing such cells to the germ cell fate.     

A new time-scale for ray-finned fish evolution

The Actinopterygii (ray-finned fishes) is the largest and most diverse vertebrate group, but little is agreed about the timing of its early evolution. Estimates using mitochondrial genomic data suggest that the major actinopterygian clades are much older than divergence dates implied by fossils. Here, the timing of the evolutionary origins of these clades is reinvestigated using morphological, and nuclear and mitochondrial genetic data. Results indicate that existing fossil-based estimates of the age of the crown-group Neopterygii, including the teleosts, Lepisosteus (gar) and Amia (bowfin), are at least 40 Myr too young. We present new palaeontological evidence that the neopterygian crown radiation is a Palaeozoic event, and demonstrate that conflicts between molecular and morphological data for the age of the Neopterygii result, in part, from missing fossil data. Although our molecular data also provide an older age estimate for the teleost crown, this range extension remains unsupported by the fossil evidence. Nuclear data from all relevant clades are used to demonstrate that the actinopterygian whole-genome duplication event is teleost-specific. While the date estimate of this event overlaps the probable range of the teleost stem group, a correlation between the genome duplication and the large-scale pattern of actinopterygian phylogeny remains elusive.     

Patterns of Evolution in the Feeding Mechanism of Actinopterygian Fishes

SYNOPSIS. Structural and functional patterns in the evolutionof the actinopterygian feeding mechanism are discussed in thecontext of the major monophyletic lineages of ray-finned fishes.A tripartite adductor mandibulae contained in a maxillary-palatoquadratechamber and a single mechanism of mandibular depression mediatedby the obliquus inferioris, sternohyoideus, and hyoid apparatusare primitive features of the Actinopterygii. Halecostome fishesare characterized by having an additional mechanism of mandibulardepression, the levator operculi—opercular series coupling,and a maxilla which swings anteriorly during prey capture. Theseinnovations provide the basis for feeding by inertial suctionwhich is the dominant mode of prey capture throughout the halecostomeradiation. A remarkably consistent kinematic profile occursin all suction-feeding halecostomes. Teleost fishes possessa number of specializations in the front jaws including a geniohyoideusmuscle, loss of the primitive suborbital adductor component,and a mobile premaxilla. Structural innovations in teleost pharyngealjaws include fusion of the dermal tooth plates with endoskeletalgill arch elements, the occurrence of a pharyngeal retractormuscle, and a shift in the origin of the pharyngohyoideus. Thesespecializations relate to increased functional versatility ofthe pharyngeal jaw apparatus as demonstrated by an electromyographicstudy of pharyngeal muscle activity in Esox and Ambloplites.The major feature of the evolution of the actinopterygian feedingmechanism is the increase in structural complexity in both thepharyngeal and front jaws. Structural diversification is a functionof the number of independent biomechanical pathways governingmovement.     

Evolution of the facial musculature in basal ray-finned fishes

Background

The facial musculature is a remarkable anatomical complex involved in vital activities of fishes, such as food capture and gill ventilation. The evolution of the facial muscles is largely unknown in most major fish lineages, such as the Actinopterygii. This megadiverse group includes all ray-finned fishes and comprises approximately half of the living vertebrate species. The Polypteriformes, Acipenseriformes, Lepisosteiformes, Amiiformes, Elopiformes, and Hiodontiformes occupy basal positions in the actinopterygian phylogeny and a comparative study of their facial musculature is crucial for understanding the cranial evolution of bony fishes (Osteichthyes) as a whole.

Results

The facial musculature of basal actinopterygians is revised, redescribed, and analyzed under an evolutionary perspective. We identified twenty main muscle components ontogenetically and evolutionarily derived from three primordial muscles. Homologies of these components are clarified and serve as basis for the proposition of a standardized and unifying myological terminology for all ray-finned fishes. The evolutionary changes in the facial musculature are optimized on the osteichthyan tree and several new synapomorphies are identified for its largest clades, including the Actinopterygii, Neopterygii, and Teleostei. Myological data alone ambiguously support the monophyly of the Holostei. A newly identified specialization constitutes the first unequivocal morphological synapomorphy for the Elopiformes. The myological survey additionally allowed a reinterpretation of the homologies of ossifications in the upper jaw of acipenseriforms.

Conclusions

The facial musculature proved to be extremely informative for the higher-level phylogeny of bony fishes. These muscles have undergone remarkable changes during the early radiation of ray-finned fishes, with significant implications for the knowledge of the musculoskeletal evolution of both derived actinopterygians and lobe-finned fishes (Sarcopterygii).

     

The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon

The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play.     

The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes.

Cytological and organismal characteristics associated with cellular DNA content underpin most adaptionist interpretations of genome size variation. Since fishes are the only group of vertebrate for which relationships between genome size and key cellular parameters are uncertain, the cytological correlates of genome size were examined in this group. The cell and nuclear areas of erythrocytes showed a highly significant positive correlation with each other and with genome size across 22 cartilaginous and 201 ray-finned fishes. Regressions remained significant at all taxonomic levels, as well as among different fish lineages. However, the results revealed that cartilaginous fishes possess higher cytogenomic ratios than ray-finned fishes, as do cold-water fishes relative to their warm-water counterparts. Increases in genome size owing to ploidy shifts were found to influence cell and nucleus size in an immediate and causative manner, an effect that persists in ancient polyploid lineages. These correlations with cytological parameters known to have important influences on organismal phenotypes support an adaptive interpretation for genome size variation in fishes.     

Cell lineage,axis formation,and the origin of germ layers in the amphipod crustacean Orchestia cavimana

Embryos of the amphipod crustacean Orchestia cavimana are examined during cleavage, gastrulation, and segmentation by using in vivo labelling. Single blastomeres of the 8- and 16-cell stages were labelled with DiI to trace cell lineages. Early cleavage follows a distinct pattern and the a/p and d/v body axes are already determined at the 4- and 8-cell stages, respectively. In these stages, the germinal rudiment and the naupliar mesoderm can be traced back to a single blastomere each. In addition, the ectoderm and the postnaupliar mesoderm are separated into right and left components. At the16-cell stage, naupliar ectoderm is divided from the postnaupliar ectoderm, and extraembryonic lineages are separated from postnaupliar mesoderm and endoderm. From our investigation, it is evident that the cleavage pattern and cell lineage of Orchestia cavimana are not of the spiral type. Furthermore, the results of the labelling show many differences to cleavage patterns and cell lineages in other crustaceans, in particular, other Malacostraca. The cleavage and cell lineage patterns of the amphipod Orchestia are certainly derived within Malacostraca, whose ancestral cleavage mode was most likely of the superficial type. On the other hand, Orchestia exhibits a stereotyped cell division pattern during formation and differentiation of the germ band that is typical for malacostracans. Hence, a derived (apomorphic) early cleavage pattern is the ontogenetic basis for an evolutionarily older cell division pattern of advanced developmental stages. O. cavimana offers the possibility to trace the lineages and the fates of cells from early developmental stages up to the formation of segmental structures, including neurogenesis at a level of resolution that is not matched by any other arthropod system.     

The expression of the imprinted gene Ipl is restricted to extra-embryonic tissues and embryonic lateral mesoderm during early mouse development

Genes with restricted expression within the developing embryo represent valuable tools as they allow distinct tissue types to be distinguished and studied. In order to identify genes that are expressed within a particular germ layer, a differential screen was performed using germ layer-specific cDNA libraries derived from gastrulation stage mouse embryos. The gene expression profiles of the germ layers were compared following the hybridisation of some 20,000 cDNA clones with probes derived from germ layer-specific Ectoderm, Mesoderm and Endoderm libraries. A cDNA clone (50c15) was identified that hybridised with the Mesoderm-derived probe but not Ectoderm or Endoderm. 50c15 derives from Ipl/Tssc3/BWR1C, an imprinted gene which in human maps to chromosome 11p15.5. This region has been associated with Beckwith-Weidemann Syndrome, Wilms' tumour and ovarian, breast and lung cancer. In the gastrulating mouse embryo, wholemount RNA in situ hybridisation revealed that Ipl expression is restricted not only to the mesodermal germ layer, but specifically to lateral mesoderm and the most posterior extent of the primitive streak from which lateral and extra-embryonic mesoderm is derived. Moreover, Ipl is expressed in extra-embryonic tissues prior to gastrulation and afterwards in extra-embryonic mesoderm, ectoderm and endoderm. This expression profile indicates that Ipl is a good molecular marker for embryonic mesoderm and extra-embryonic tissues. In addition heterotopic grafting studies indicate that nascent mesoderm, which expresses Ipl, is restricted in its potential and therefore may be committed to its fate.